repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
pyro | pyro/infer/reparam/transform.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
import pyro
import pyro.distributions as dist
from .reparam import Reparam
class TransformReparam(Reparam):
"""
Reparameterizer for
:class:`pyro.distributions.torch.TransformedDistribution` latent varia... | 59 | 1,789 |
pyro | pyro/infer/reparam/split.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import torch
import pyro
import pyro.distributions as dist
import pyro.poutine as poutine
from pyro.distributions.torch_distribution import TorchDistributionMixin
from pyro.ops.tensor_utils import broadcast_tensors_without_dim
from .... | 141 | 5,504 |
pyro | pyro/infer/reparam/stable.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
import pyro
import pyro.distributions as dist
from pyro.distributions.stable import _standard_stable, _unsafe_standard_stable
from pyro.infer.util import is_validation_enabled
from .reparam import Repara... | 270 | 10,548 |
pyro | pyro/infer/reparam/haar.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.distributions.transforms.haar import HaarTransform
from .unit_jacobian import UnitJacobianReparam
class HaarReparam(UnitJacobianReparam):
"""
Haar wavelet reparameterizer, using a
:class:`~pyro.distributions.tr... | 37 | 1,594 |
pyro | pyro/infer/reparam/conjugate.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import pyro
import pyro.distributions as dist
import pyro.poutine as poutine
from .reparam import Reparam
class ConjugateReparam(Reparam):
"""
EXPERIMENTAL Reparameterize to a conjugate updated distribution.
This update... | 109 | 4,315 |
pyro | pyro/infer/reparam/softmax.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import torch
import pyro
import pyro.distributions as dist
from .reparam import Reparam
class GumbelSoftmaxReparam(Reparam):
"""
Reparametrizer for :class:`~pyro.distributions.RelaxedOneHotCategorical`
latent variables.... | 61 | 1,869 |
pyro | pyro/infer/reparam/studentt.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import pyro
import pyro.distributions as dist
from .reparam import Reparam
class StudentTReparam(Reparam):
"""
Auxiliary variable reparameterizer for
:class:`~pyro.distributions.StudentT` random variables.
This is u... | 45 | 1,477 |
pyro | pyro/infer/reparam/neutra.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from contextlib import ExitStack
from torch.distributions import biject_to
import pyro
import pyro.distributions as dist
from pyro import poutine
from pyro.distributions.util import sum_rightmost
from pyro.infer.autoguide.guides ... | 142 | 5,549 |
pyro | pyro/infer/reparam/strategies.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
"""
These reparametrization strategies are registered with
:func:`~pyro.poutine.reparam_messenger.register_reparam_strategy` and are
accessed by name via ``poutine.reparam(config=name_of_strategy)`` .
See :func:`~pyro.poutine.handlers.... | 217 | 7,528 |
pyro | pyro/infer/reparam/__init__.py | .py | # Copyright Contributors to the Pyro project.
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from .conjugate import ConjugateReparam
from .discrete_cosine import DiscreteCosineReparam
from .haar import HaarReparam
from .hmm import LinearHMMReparam
from .loc_scale import LocScal... | 41 | 1,239 |
pyro | pyro/infer/reparam/unit_jacobian.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from contextlib import ExitStack
from torch.distributions import biject_to
from torch.distributions.transforms import ComposeTransform
import pyro
import pyro.distributions as dist
from pyro.poutine.plate_messenger import block_plate... | 103 | 3,913 |
pyro | pyro/infer/reparam/projected_normal.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import torch
import pyro
import pyro.distributions as dist
from pyro.ops.tensor_utils import safe_normalize
from .reparam import Reparam
class ProjectedNormalReparam(Reparam):
"""
Reparametrizer for :class:`~pyro.distributi... | 56 | 1,697 |
pyro | pyro/infer/reparam/structured.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from contextlib import ExitStack
import pyro.distributions as dist
from pyro import poutine
from pyro.infer.autoguide.structured import AutoStructured
from pyro.poutine.plate_messenger import block_plate
from .reparam import Reparam
... | 107 | 4,312 |
pyro | pyro/infer/reparam/loc_scale.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from torch.distributions import constraints
import pyro
import pyro.distributions as dist
from pyro.distributions.util import is_identically_one, is_validation_enabled
from .reparam import Reparam
class LocScaleRep... | 101 | 3,812 |
pyro | pyro/infer/reparam/discrete_cosine.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.distributions.transforms.discrete_cosine import DiscreteCosineTransform
from .unit_jacobian import UnitJacobianReparam
class DiscreteCosineReparam(UnitJacobianReparam):
"""
Discrete Cosine reparameterizer, using a
... | 43 | 2,076 |
pyro | pyro/infer/autoguide/utils.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import functools
from contextlib import contextmanager
from pyro import poutine
from pyro.nn.module import PyroModule
def _product(shape):
"""
Computes the product of the dimensions of a given shape tensor
"""
re... | 87 | 2,979 |
pyro | pyro/infer/autoguide/effect.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from operator import attrgetter
from typing import Callable, Optional, Tuple, Union
import torch
from torch.distributions import biject_to, constraints
import pyro.distributions as dist
from pyro.distributions.distribution import Dis... | 456 | 19,656 |
pyro | pyro/infer/autoguide/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from pyro.infer.autoguide.effect import (
AutoHierarchicalNormalMessenger,
AutoMessenger,
AutoNormalMessenger,
AutoRegressiveMessenger,
)
from pyro.infer.autoguide.gaussian import AutoGaussian
from pyro.infer.autogu... | 67 | 1,618 |
pyro | pyro/infer/autoguide/gaussian.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import itertools
from abc import ABCMeta, abstractmethod
from collections import OrderedDict, defaultdict
from contextlib import ExitStack
from operator import attrgetter
from types import SimpleNamespace
from typing import Callable, D... | 631 | 26,020 |
pyro | pyro/infer/autoguide/initialization.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
r"""
The pyro.infer.autoguide.initialization module contains initialization functions for
automatic guides.
The standard interface for initialization is a function that inputs a Pyro
trace ``site`` dict and returns an appropriatel... | 258 | 8,271 |
pyro | pyro/infer/autoguide/guides.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
The :mod:`pyro.infer.autoguide` module provides algorithms to automatically
generate guides from simple models, for use in :class:`~pyro.infer.svi.SVI`.
For example to generate a mean field Gaussian guide::
def model():
... | 1,289 | 49,219 |
pyro | pyro/infer/autoguide/structured.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import OrderedDict, defaultdict
from contextlib import ExitStack
from operator import attrgetter
from types import SimpleNamespace
from typing import Callable, Dict, Optional, Union
import torch
from torch.distributio... | 377 | 16,329 |
pyro | pyro/infer/mcmc/logger.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import json
import logging
import os
import sys
from collections import OrderedDict
from tqdm import tqdm
from tqdm.auto import tqdm as tqdm_nb
try:
get_ipython
ipython_env = True
except NameError:
ipython_env = False... | 276 | 9,270 |
pyro | pyro/infer/mcmc/mcmc_kernel.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from abc import ABCMeta, abstractmethod
class MCMCKernel(object, metaclass=ABCMeta):
def setup(self, warmup_steps, *args, **kwargs):
r"""
Optional method to set up any state required at the start of the
... | 81 | 2,347 |
pyro | pyro/infer/mcmc/util.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import functools
import traceback as tb
import warnings
from collections import OrderedDict, defaultdict
from functools import partial, reduce
from itertools import product
import torch
from opt_einsum import shared_intermediates
... | 843 | 33,005 |
pyro | pyro/infer/mcmc/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from pyro.infer.mcmc.adaptation import ArrowheadMassMatrix, BlockMassMatrix
from pyro.infer.mcmc.api import MCMC, StreamingMCMC
from pyro.infer.mcmc.hmc import HMC
from pyro.infer.mcmc.nuts import NUTS
from pyro.infer.mcmc.rwkernel... | 19 | 490 |
pyro | pyro/infer/mcmc/hmc.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
from collections import OrderedDict
import torch
import pyro
import pyro.distributions as dist
from pyro.distributions.testing.fakes import NonreparameterizedNormal
from pyro.distributions.util import scalar_like
from... | 453 | 18,825 |
pyro | pyro/infer/mcmc/rwkernel.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import math
from collections import OrderedDict
import torch
import pyro
import pyro.distributions as dist
from pyro.infer.mcmc.mcmc_kernel import MCMCKernel
from pyro.infer.mcmc.util import initialize_model
class RandomWalkKernel(... | 144 | 4,827 |
pyro | pyro/infer/mcmc/api.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
This module offers a modified interface for MCMC inference with the following objectives:
- making MCMC independent of Pyro specific trace data structure, to facilitate
integration with other PyTorch based libraries.
- ... | 796 | 29,289 |
pyro | pyro/infer/mcmc/nuts.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from collections import namedtuple
import pyro
import pyro.distributions as dist
from pyro.distributions.util import scalar_like
from pyro.infer.autoguide import init_to_uniform
from pyro.infer.mcmc.hmc import HMC
from pyro.ops.in... | 523 | 21,893 |
pyro | pyro/infer/mcmc/adaptation.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
from collections import namedtuple
import torch
import pyro
from pyro.ops.arrowhead import (
SymmArrowhead,
sqrt,
triu_gram,
triu_inverse,
triu_matvecmul,
)
from pyro.ops.dual_averaging import Dual... | 580 | 23,000 |
pyro | pyro/ops/arrowhead.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import namedtuple
import torch
SymmArrowhead = namedtuple("SymmArrowhead", ["top", "bottom_diag"])
TriuArrowhead = namedtuple("TriuArrowhead", ["top", "bottom_diag"])
def sqrt(x):
"""
EXPERIMENTAL Computes ... | 128 | 4,306 |
pyro | pyro/ops/packed.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from pyro.distributions.util import is_identically_one
from pyro.util import ignore_jit_warnings
def pack(value, dim_to_symbol):
"""
Converts an unpacked tensor to a packed tensor.
:param v... | 201 | 6,350 |
pyro | pyro/ops/jit.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import argparse
import warnings
import weakref
import torch
import pyro
import pyro.poutine as poutine
from pyro.util import ignore_jit_warnings, optional, timed
def _hash(value, allow_id):
try:
hash(value)
... | 164 | 5,970 |
pyro | pyro/ops/stats.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import numbers
from typing import Callable, List, Optional, Tuple, Union
import torch
from torch.fft import irfft, rfft
from .tensor_utils import next_fast_len
def _compute_chain_variance_stats(input):
# compute... | 606 | 23,706 |
pyro | pyro/ops/ssm_gp.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from torch.distributions import constraints
from pyro.nn import PyroModule, PyroParam, pyro_method
root_three = math.sqrt(3.0)
root_five = math.sqrt(5.0)
five_thirds = 5.0 / 3.0
class MaternKernel(Pyro... | 169 | 6,648 |
pyro | pyro/ops/indexing.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
def _is_batched(arg):
return isinstance(arg, torch.Tensor) and arg.dim()
def _flatten(args, out):
if isinstance(args, tuple):
for arg in args:
_flatten(arg, out)
else:
# Comb... | 218 | 7,458 |
pyro | pyro/ops/tensor_utils.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from torch.fft import irfft, rfft
from .. import settings
_ROOT_TWO_INVERSE = 1.0 / math.sqrt(2.0)
CHOLESKY_RELATIVE_JITTER = 4.0 # in units of finfo.eps
@settings.register("cholesky_relative_jitter",... | 505 | 17,017 |
pyro | pyro/ops/integrator.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import warnings
from typing import Callable, Dict
from torch.autograd import grad
# Registry for exception handlers that can be used to catch certain failures
# during computation of `potential_fn` within `potential_grad`.
_EXCEP... | 130 | 5,119 |
pyro | pyro/ops/dual_averaging.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
class DualAveraging:
"""
Dual Averaging is a scheme to solve convex optimization problems. It belongs
to a class of subgradient methods which uses subgradients to update parameters
(in primal space) of a model. Und... | 80 | 3,402 |
pyro | pyro/ops/special.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import functools
import math
import operator
import weakref
from typing import Dict
import numpy as np
import torch
from numpy.polynomial.hermite import hermgauss
class _SafeLog(torch.autograd.Function):
@staticmethod
def fo... | 219 | 7,034 |
pyro | pyro/ops/newton.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from torch.autograd import grad
from pyro.ops.linalg import eig_3d, rinverse
from pyro.util import warn_if_nan
def newton_step(loss, x, trust_radius=None):
"""
Performs a Newton update step to minimize loss ... | 247 | 9,520 |
pyro | pyro/ops/gaussian.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
from typing import Optional, Tuple, Union
import torch
from torch.distributions.utils import lazy_property
from torch.nn.functional import pad
from pyro.distributions.util import broadcast_shape
from pyro.ops.tensor_u... | 716 | 28,119 |
pyro | pyro/ops/contract.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import itertools
import warnings
from collections import OrderedDict, defaultdict
import opt_einsum
import torch
from opt_einsum import shared_intermediates
from pyro.ops.rings import BACKEND_TO_RING, LogRing
from pyro.util impor... | 575 | 22,550 |
pyro | pyro/ops/provenance.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from functools import partial, singledispatch
from typing import Tuple, TypeVar
import torch
from torch.utils._pytree import tree_flatten, tree_map, tree_unflatten
_Tensor = TypeVar("_Tensor", bound=torch.Tensor)
class ProvenanceTe... | 175 | 5,765 |
pyro | pyro/ops/welford.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
class WelfordCovariance:
"""
Implements Welford's online scheme for estimating (co)variance (see :math:`[1]`).
Useful for adapting diagonal and dense mass structures for HMC.
**References**
[1] ... | 102 | 3,409 |
pyro | pyro/ops/hessian.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
def hessian(y, xs):
"""
Convenience method for computing hessians. Note that this is slow in high
dimensions because computing hessians in a reverse-mode AD library like
PyTorch is inherently slow (no... | 23 | 673 |
pyro | pyro/ops/streaming.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import copy
from abc import ABC, abstractmethod
from collections import defaultdict
from typing import Any, Callable, Dict, Hashable, Union
import torch
from pyro.ops.welford import WelfordCovariance
class StreamingStats(ABC):
... | 278 | 8,903 |
pyro | pyro/ops/linalg.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import warnings
from contextlib import contextmanager
import torch
@contextmanager
def ignore_torch_deprecation_warnings():
with warnings.catch_warnings():
# Ignore deprecation warning until funsor update... | 107 | 3,577 |
pyro | pyro/ops/gamma_gaussian.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from torch.distributions.utils import lazy_property
from torch.nn.functional import pad
from pyro.distributions.multivariate_studentt import MultivariateStudentT
from pyro.distributions.torch import Multi... | 469 | 17,941 |
pyro | pyro/ops/rings.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import weakref
from abc import ABCMeta, abstractmethod
import torch
from pyro.ops.einsum import contract
from pyro.ops.einsum.adjoint import SAMPLE_SYMBOL, Backward
from pyro.util import ignore_jit_warnings
class Ring(object, m... | 339 | 11,388 |
pyro | pyro/ops/einsum/torch_marginal.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import pyro.ops.einsum.torch_log
from pyro.ops.einsum.adjoint import Backward, transpose
from pyro.ops.einsum.util import Tensordot
class _EinsumBackward(Backward):
def __init__(self, equation, operands):
self.equatio... | 63 | 2,234 |
pyro | pyro/ops/einsum/util.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0 AND MIT
EINSUM_SYMBOLS_BASE = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
class Tensordot:
"""
Creates a tensordot implementation from an einsum implementation.
"""
def __init__(self, einsum):
... | 60 | 1,901 |
pyro | pyro/ops/einsum/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import opt_einsum
from pyro.util import ignore_jit_warnings
_PATH_CACHE = {}
def contract_expression(equation, *shapes, **kwargs):
"""
Wrapper around :func:`opt_einsum.contract_expression` that optionally uses
Pyro'... | 50 | 1,486 |
pyro | pyro/ops/einsum/torch_log.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from pyro.ops.einsum.util import Tensordot
from pyro.ops.special import safe_log
def transpose(a, axes):
return a.permute(axes)
def einsum(equation, *operands):
"""
Log-sum-exp implementation of einsum... | 61 | 2,010 |
pyro | pyro/ops/einsum/adjoint.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import weakref
from abc import ABCMeta, abstractmethod
import torch
from pyro.ops import packed
from pyro.util import jit_iter
SAMPLE_SYMBOL = " " # must be unique and precede alphanumeric characters
class Backward(object, me... | 151 | 4,971 |
pyro | pyro/ops/einsum/torch_sample.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import operator
from functools import reduce
import pyro.distributions as dist
import pyro.ops.einsum.torch_log
from pyro.ops import packed
from pyro.ops.einsum.adjoint import (
Backward,
einsum_backward_sample,
transp... | 80 | 2,736 |
pyro | pyro/ops/einsum/torch_map.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import operator
from functools import reduce
from pyro.ops import packed
from pyro.ops.einsum.adjoint import (
Backward,
einsum_backward_sample,
transpose,
unflatten,
)
from pyro.ops.einsum.util import Tensordot
... | 62 | 1,952 |
pyro | pyro/contrib/autoguide.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import warnings
from pyro.infer.autoguide import * # noqa F403
warnings.warn(
"pyro.contrib.autoguide has moved to pyro.infer.autoguide. "
"The contrib alias will stop working in Pyro 0.5.",
DeprecationWarning,
)
| 13 | 317 |
pyro | pyro/contrib/util.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import weakref
from collections import OrderedDict
import torch
import pyro
def get_indices(labels, sizes=None, tensors=None):
indices = []
start = 0
if sizes is None:
sizes = OrderedDict([(l, t.shape[0]) fo... | 98 | 2,800 |
pyro | pyro/contrib/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
r"""
Contributed Code
================
.. warning:: Code in ``pyro.contrib`` is under various stages of development.
This code makes no guarantee about maintaining backwards compatibility.
"""
from pyro.contrib import (
a... | 43 | 693 |
pyro | pyro/contrib/minipyro.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
Mini Pyro
---------
This file contains a minimal implementation of the Pyro Probabilistic
Programming Language. The API (method signatures, etc.) match that of
the full implementation as closely as possible. This file is indep... | 407 | 15,592 |
pyro | pyro/contrib/zuko.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
"""
This file contains helpers to use `Zuko <https://zuko.readthedocs.io/>`_-based
normalizing flows within Pyro piplines.
Accompanying tutorials can be found at `tutorial/svi_flow_guide.ipynb` and
`tutorial/vae_flow_prior.ipynb`.
"""... | 82 | 2,230 |
pyro | pyro/contrib/cevae/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
This module implements the Causal Effect Variational Autoencoder [1], which
demonstrates a number of innovations including:
- a generative model for causal effect inference with hidden confounders;
- a model and guide with twi... | 663 | 23,080 |
pyro | pyro/contrib/funsor/__init__.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import pyroapi
from pyro.contrib.funsor.handlers import condition, do, markov, vectorized_markov
from pyro.contrib.funsor.handlers import plate as _plate
from pyro.contrib.funsor.handlers.primitives import to_data, to_funsor
from pyro... | 59 | 1,223 |
pyro | pyro/contrib/funsor/handlers/runtime.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import Counter, OrderedDict, namedtuple
from enum import Enum
class StackFrame:
"""
Consistent bidirectional mapping between integer positional dimensions and names.
Can be queried like a dictionary (``va... | 238 | 8,558 |
pyro | pyro/contrib/funsor/handlers/enum_messenger.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
"""
This file contains reimplementations of some of Pyro's core enumeration machinery,
which should eventually be drop-in replacements for the current versions.
"""
import functools
import math
from collections import OrderedDict
imp... | 267 | 9,728 |
pyro | pyro/contrib/funsor/handlers/__init__.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.poutine import ( # noqa: F401
block,
condition,
do,
escape,
infer_config,
mask,
reparam,
scale,
seed,
uncondition,
)
from pyro.poutine.handlers import _make_handler
from .enum_messeng... | 60 | 1,408 |
pyro | pyro/contrib/funsor/handlers/plate_messenger.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import OrderedDict
from numbers import Number
import funsor
from pyro.contrib.funsor.handlers.named_messenger import (
DimRequest,
DimType,
GlobalNamedMessenger,
NamedMessenger,
)
from pyro.contrib.fu... | 384 | 15,224 |
pyro | pyro/contrib/funsor/handlers/primitives.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import pyro.poutine.runtime
from pyro.contrib.funsor.handlers.runtime import _DIM_STACK, DimRequest, DimType
@pyro.poutine.runtime.effectful(type="to_funsor")
def to_funsor(x, output=None, dim_to_name=None, dim_type=DimType.LOCAL):
... | 30 | 1,076 |
pyro | pyro/contrib/funsor/handlers/replay_messenger.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.contrib.funsor.handlers.primitives import to_data
from pyro.poutine.replay_messenger import ReplayMessenger as OrigReplayMessenger
class ReplayMessenger(OrigReplayMessenger):
"""
This version of :class:`~ReplayMesse... | 42 | 1,806 |
pyro | pyro/contrib/funsor/handlers/named_messenger.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import OrderedDict
from contextlib import ExitStack
from pyro.contrib.funsor.handlers.runtime import (
_DIM_STACK,
DimRequest,
DimType,
StackFrame,
)
from pyro.poutine.reentrant_messenger import Reentr... | 201 | 7,623 |
pyro | pyro/contrib/funsor/handlers/trace_messenger.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import funsor
import torch
from pyro.contrib.funsor.handlers.primitives import to_funsor
from pyro.contrib.funsor.handlers.runtime import _DIM_STACK
from pyro.poutine.subsample_messenger import _Subsample
from pyro.poutine.trace_messe... | 84 | 3,632 |
pyro | pyro/contrib/funsor/infer/elbo.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import pyro.ops.jit
from pyro.infer import ELBO as _OrigELBO
from pyro.util import ignore_jit_warnings
class ELBO(_OrigELBO):
def _get_trace(self, *args, **kwargs):
raise ValueError("shouldn't be here!")
def differen... | 46 | 1,652 |
pyro | pyro/contrib/funsor/infer/tracetmc_elbo.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import contextlib
import funsor
from pyro.contrib.funsor import to_data
from pyro.contrib.funsor.handlers import enum, plate, replay, trace
from pyro.contrib.funsor.infer.elbo import ELBO, Jit_ELBO
from pyro.contrib.funsor.infer.trac... | 55 | 1,916 |
pyro | pyro/contrib/funsor/infer/__init__.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.infer import SVI, config_enumerate # noqa: F401
from .discrete import infer_discrete # noqa: F401
from .elbo import ELBO # noqa: F401
from .trace_elbo import JitTrace_ELBO, Trace_ELBO # noqa: F401
from .traceenum_elbo im... | 16 | 514 |
pyro | pyro/contrib/funsor/infer/trace_elbo.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import contextlib
import funsor
from pyro.contrib.funsor import to_data, to_funsor
from pyro.contrib.funsor.handlers import enum, plate, replay, trace
from pyro.contrib.funsor.infer import config_enumerate
from pyro.distributions.uti... | 53 | 1,724 |
pyro | pyro/contrib/funsor/infer/discrete.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import functools
import funsor
from pyro.contrib.funsor.handlers import enum, replay, trace
from pyro.contrib.funsor.handlers.enum_messenger import _get_support_value
from pyro.contrib.funsor.infer.traceenum_elbo import terms_from_tr... | 73 | 2,921 |
pyro | pyro/contrib/funsor/infer/traceenum_elbo.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import contextlib
import funsor
from funsor.adjoint import AdjointTape
from funsor.sum_product import _partition
from pyro.contrib.funsor import to_data, to_funsor
from pyro.contrib.funsor.handlers import enum, plate, replay, trace
f... | 284 | 12,731 |
pyro | pyro/contrib/conjugate/infer.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from collections import defaultdict
import torch
import pyro.distributions as dist
from pyro import poutine
from pyro.distributions.util import sum_leftmost
from pyro.poutine.messenger import Messenger
from pyro.poutine.util impo... | 245 | 9,073 |
pyro | pyro/contrib/epidemiology/models.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import re
import torch
from torch.nn.functional import pad
import pyro
import pyro.distributions as dist
from .compartmental import CompartmentalModel
from .distributions import binomial_dist, infection_dist
class SimpleSIRModel(C... | 1,286 | 51,173 |
pyro | pyro/contrib/epidemiology/distributions.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import math
from contextlib import contextmanager
import torch
from torch.distributions.utils import broadcast_all
import pyro.distributions as dist
from pyro.distributions.util import is_validation_enabled
_RELAX = False
_RELAX_MIN... | 342 | 13,549 |
pyro | pyro/contrib/epidemiology/util.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import numpy as np
import torch
import pyro
import pyro.distributions as dist
import pyro.poutine as poutine
from pyro.distributions.util import broadcast_shape
from pyro.ops.special import safe_log
def clamp(tensor, *, min=None, ma... | 380 | 10,993 |
pyro | pyro/contrib/epidemiology/__init__.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.distributions.coalescent import bio_phylo_to_times
from .compartmental import CompartmentalModel
from .distributions import beta_binomial_dist, binomial_dist, infection_dist
__all__ = [
"CompartmentalModel",
"beta_b... | 16 | 406 |
pyro | pyro/contrib/epidemiology/compartmental.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import functools
import logging
import operator
import re
import warnings
from abc import ABC, abstractmethod
from collections import OrderedDict
from contextlib import ExitStack, contextmanager
from functools import reduce
from timeit... | 1,250 | 49,835 |
pyro | pyro/contrib/bnn/utils.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
def xavier_uniform(D_in, D_out):
scale = math.sqrt(6.0 / float(D_in + D_out))
noise = torch.rand(D_in, D_out)
return 2.0 * scale * noise - scale
def adjoin_ones_vector(x):
return torch.... | 21 | 490 |
pyro | pyro/contrib/bnn/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from pyro.contrib.bnn.hidden_layer import HiddenLayer
__all__ = [
"HiddenLayer",
]
| 9 | 177 |
pyro | pyro/contrib/bnn/hidden_layer.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
import torch.nn.functional as F
from torch.distributions.utils import lazy_property
from pyro.contrib.bnn.utils import adjoin_ones_vector
from pyro.distributions.torch_distribution import TorchDistribution
class Hid... | 127 | 5,384 |
pyro | pyro/contrib/autoname/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
The :mod:`pyro.contrib.autoname` module provides tools for automatically
generating unique, semantically meaningful names for sample sites.
"""
from pyro.contrib.autoname import named
from pyro.contrib.autoname.autoname import... | 20 | 487 |
pyro | pyro/contrib/autoname/autoname.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from collections import defaultdict
from collections.abc import Iterable
from functools import singledispatch
import pyro
from pyro.poutine.handlers import _make_handler
from pyro.poutine.reentrant_messenger import ReentrantMessenger
... | 179 | 5,100 |
pyro | pyro/contrib/autoname/scoping.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
``pyro.contrib.autoname.scoping`` contains the implementation of
:func:`pyro.contrib.autoname.scope`, a tool for automatically appending
a semantically meaningful prefix to names of sample sites.
"""
import functools
from pyr... | 193 | 6,483 |
pyro | pyro/contrib/autoname/named.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
The ``pyro.contrib.named`` module is a thin syntactic layer on top of Pyro. It
allows Pyro models to be written to look like programs with operating on Python
data structures like ``latent.x.sample_(...)``, rather than program... | 255 | 8,625 |
pyro | pyro/contrib/oed/util.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from pyro.contrib.oed.glmm import analytic_posterior_cov
from pyro.contrib.util import get_indices
from pyro.infer.autoguide.utils import mean_field_entropy
def linear_model_ground_truth(
model, des... | 38 | 1,230 |
pyro | pyro/contrib/oed/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""Tasks such as choosing the next question to ask in a psychology study, designing an election polling
strategy, and deciding which compounds to synthesize and test in biological sciences are all fundamentally asking the
same ques... | 73 | 3,789 |
pyro | pyro/contrib/oed/eig.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import warnings
import torch
import pyro
from pyro import poutine
from pyro.contrib.oed.search import Search
from pyro.contrib.util import lexpand
from pyro.infer import SVI, EmpiricalMarginal, Importance
from pyro.in... | 1,200 | 44,795 |
pyro | pyro/contrib/oed/search.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import queue
import pyro.poutine as poutine
from pyro.infer.abstract_infer import TracePosterior
###################################
# Search borrowed from RSA example
###################################
class Search(TracePoste... | 31 | 867 |
pyro | pyro/contrib/oed/glmm/glmm.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import warnings
from collections import OrderedDict
from contextlib import ExitStack
from functools import partial
import torch
from torch.distributions import constraints
from torch.distributions.transforms import AffineTransform... | 468 | 16,376 |
pyro | pyro/contrib/oed/glmm/__init__.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
"""
.. warning :: This module will eventually be deprecated in favor of `brmp <https://github.com/pyro-ppl/brmp/>`_
The :mod:`pyro.contrib.oed.glmm` module provides models and guides for
generalised linear mixed models (GLMM). It ... | 41 | 1,551 |
pyro | pyro/contrib/oed/glmm/guides.py | .py | # Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from contextlib import ExitStack
import torch
from torch import nn
import pyro
import pyro.distributions as dist
from pyro import poutine
from pyro.contrib.util import (
iter_plates_to_shape,
lexpand,
rmv,
rtril,
... | 314 | 11,368 |
pyro | pyro/contrib/randomvariable/__init__.py | .py | # Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
from pyro.contrib.randomvariable.random_variable import RandomVariable
__all__ = [
"RandomVariable",
]
| 9 | 193 |
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